diff --git a/docs/code/idlaurorax_api_reference/data/aurorax_list_datasets.md b/docs/code/idlaurorax_api_reference/data/aurorax_list_datasets.md
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+---
+hide:
+  - toc
+---
+
+# aurorax_list_datasets
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_LIST_DATASETS
+;
+; PURPOSE:
+;       Retrieve list of available datasets for which you can
+;       download data.
+;
+; EXPLANATION:
+;       Retrieve information about available datasets, including provider,
+;       short+long descriptions, and DOI details. Optional parameters are
+;       used to filter for certain matching datasets.
+;
+; CALLING SEQUENCE:
+;       aurorax_list_datasets()
+;
+; PARAMETERS:
+;       name         dataset name for filter on, case-sensitive and partial
+;                    matches are allowed. Optional.
+;
+; OUTPUT
+;       the found datasets
+;
+; OUTPUT TYPE:
+;       a list of structs
+;
+; EXAMPLES:
+;       datasets = aurorax_list_datasets()
+;       datasets = aurorax_list_datasets(name='THEMIS_ASI')
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/data/aurorax_list_observatories.md b/docs/code/idlaurorax_api_reference/data/aurorax_list_observatories.md
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+---
+hide:
+  - toc
+---
+
+# aurorax_list_observatories
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_LIST_OVSERVATORIES
+;
+; PURPOSE:
+;       Retrieve list of available observatories where an instrument exists.
+;
+; EXPLANATION:
+;       Retrieve information about observatories, including full name, geodetic
+;       latitude and longitude. Optional parameters are used to filter for certain
+;       matching observatories.
+;
+; CALLING SEQUENCE:
+;       aurorax_list_observatories(instrument_array)
+;
+; PARAMETERS:
+;       insrument_array     the insrument array. Possible values are 'themis_asi',
+;                           'rego', 'trex_rgb', 'trex_nir', and 'trex_blue'.
+;       uid                 site unique identifier to filter on, optional
+;
+; OUTPUT
+;       the found observatories
+;
+; OUTPUT TYPE:
+;       a list of structs
+;
+; EXAMPLES:
+;       observatories = aurorax_list_observatories('themis_asi')
+;       observatories = aurorax_list_datasets('trex_rgb', uid='gill')
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/data/aurorax_ucalgary_download.md b/docs/code/idlaurorax_api_reference/data/aurorax_ucalgary_download.md
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+---
+hide:
+  - toc
+---
+
+# aurorax_ucalgary_download
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_UCALGARY_DOWNLOAD
+;
+; PURPOSE:
+;       Download data from the UCalgary Open Data Platform
+;
+; EXPLANATION:
+;       Download data from the UCalgary Open Data Platform, for the given
+;       dataset, timeframe, and optional site/device.
+;
+; CALLING SEQUENCE:
+;       aurorax_ucalgary_download(dataset_name, start_ts, end_ts)
+;
+; PARAMETERS:
+;       dataset_name       name of the dataset to download data for
+;       start_ts           start timestamp, format as ISO time string (YYYY-MM-DDTHH:MM:SS)
+;       end_ts             end timestamp, format as ISO time string (YYYY-MM-DDTHH:MM:SS)
+;       site_uid           unique 4-letter site UID to filter on (e.g., atha, gill, fsmi), optional
+;       device_uid         unique device UID to filter on (e.g., themis08, rgb-09), optional
+;       download_path      path to save data to, default is your home directory; optional
+;
+; KEYWORDS:
+;       /OVERWRITE         download the files regardless of them existing locally already
+;       /QUIET             no print messages, data download will be silent
+;
+; OUTPUT
+;       information about the downloaded data
+;
+; OUTPUT TYPE:
+;       a struct
+;
+; EXAMPLES:
+;       d = aurorax_ucalgary_download('THEMIS_ASI_RAW','2022-01-01T06:00:00','2022-01-01T06:59:59',site_uid='atha')
+;       d = aurorax_ucalgary_download('TREX_RGB_RAW_NOMINAL','2022-01-01T06:00:00','2022-01-01T06:00:00',/overwrite)
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/data/aurorax_ucalgary_download_best_skymap.md b/docs/code/idlaurorax_api_reference/data/aurorax_ucalgary_download_best_skymap.md
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+---
+hide:
+  - toc
+---
+
+# aurorax_ucalgary_download_best_skymap
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_UCALGARY_DOWNLOAD_BEST_SKYMAP
+;
+; PURPOSE:
+;       Download the best skymap for the corresponding parameters
+;
+; EXPLANATION:
+;       Download the best skymap for the given dataset name, timestamp, and site UID
+;
+; CALLING SEQUENCE:
+;       aurorax_ucalgary_download_best_skymap(dataset_name, site_uid, time_stamp)
+;
+; PARAMETERS:
+;       dataset_name       name of the skymap dataset to download data for
+;       site_uid           unique 4-letter site UID to retrieve skymap for
+;       time_stamp         timestamp, format as ISO time string (YYYY-MM-DDTHH:MM:SS)
+;       download_path      path to save data to, default is your home directory; optional
+;
+; KEYWORDS:
+;       /OVERWRITE         download the skymap files regardless of them existing locally already
+;       /QUIET             no print messages, data download will be silent
+;
+; OUTPUT
+;       information about the downloaded data
+;
+; OUTPUT TYPE:
+;       a struct
+;
+; EXAMPLES:
+;       d = aurorax_ucalgary_download_best_skymap('THEMIS_ASI_SKYMAP_IDLSAV','atha','2020-01-01T00:00:00')
+;       d = aurorax_ucalgary_download_best_skymap('TREX_RGB_SKYMAP_IDLSAV','gill','2023-02-01T06:00:00',/overwrite)
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/data/aurorax_ucalgary_get_urls.md b/docs/code/idlaurorax_api_reference/data/aurorax_ucalgary_get_urls.md
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+---
+hide:
+  - toc
+---
+
+# aurorax_ucalgary_get_urls
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_UCALGARY_GET_URLS
+;
+; PURPOSE:
+;       Retrieve list of URLS that can be downloaded from the UCalgary
+;       Open Data Platform.
+;
+; EXPLANATION:
+;       Retrieve the URLs of files available for download from the UCalgary
+;       Open Data Platform, for the given dataset, timeframe, and optional
+;       site/device. This function is used by the aurorax_ucalgary_download()
+;       function.
+;
+; CALLING SEQUENCE:
+;       aurorax_ucalgary_get_urls(dataset_name, start_ts, end_ts)
+;
+; PARAMETERS:
+;       dataset_name       name of the dataset to get URLs of data files for
+;       start_ts           start timestamp, format as ISO time string (YYYY-MM-DDTHH:MM:SS)
+;       end_ts             end timestamp, format as ISO time string (YYYY-MM-DDTHH:MM:SS)
+;       site_uid           unique 4-letter site UID to filter on (e.g., atha, gill, fsmi), optional
+;       device_uid         unique device UID to filter on (e.g., themis08, rgb-09), optional
+;
+; OUTPUT
+;       information about the available URLs of data files
+;
+; OUTPUT TYPE:
+;       a struct
+;
+; EXAMPLES:
+;       u = aurorax_ucalgary_get_urls('THEMIS_ASI_RAW','2022-01-01T06:00:00','2022-01-01T06:59:59',site_uid='atha')
+;       u = aurorax_ucalgary_get_urls('TREX_RGB_RAW_NOMINAL','2022-01-01T06:00:00','2022-01-01T06:00:00')
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/data/aurorax_ucalgary_is_read_supported.md b/docs/code/idlaurorax_api_reference/data/aurorax_ucalgary_is_read_supported.md
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+---
+hide:
+  - toc
+---
+
+# aurorax_ucalgary_is_read_supported
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_UCALGARY_IS_READ_SUPPORTED
+;
+; PURPOSE:
+;       Determine if a given dataset is supported in the aurorax_ucalgary_read()
+;       function.
+;
+; EXPLANATION:
+;       Some datasets provided by UCalgary require special readfile routines. This
+;       function provides the ability to programmatically determine if a dataset
+;       is supported in the aurorax_ucalgary_read() function.
+;
+;       Some datasets are simple enough for special read routines to be needed. For
+;       example, 'THEMIS_ASI_DAILY_KEOGRAM_JPG', can be read in using the built-in
+;       READ_JPEG procedure.
+;
+; CALLING SEQUENCE:
+;       aurorax_ucalgary_is_read_supported(dataset_name)
+;
+; PARAMETERS:
+;       dataset_name       name of the dataset check for read support
+;
+; OUTPUT
+;       0 for False, 1 for True
+;
+; OUTPUT TYPE:
+;       integer
+;
+; EXAMPLES:
+;       supported = aurorax_ucalgary_is_read_supported('THEMIS_ASI_RAW')
+;       supported = aurorax_ucalgary_is_read_supported('THEMIS_ASI_DAILY_KEOGRAM_JPG')
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/data/aurorax_ucalgary_read.md b/docs/code/idlaurorax_api_reference/data/aurorax_ucalgary_read.md
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+---
+hide:
+  - toc
+---
+
+# aurorax_ucalgary_read
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_UCALGARY_READ
+;
+; PURPOSE:
+;       Read data downloaded from the UCalgary Open Data Platform
+;
+; EXPLANATION:
+;       Read data files that were dowloaded from the UCalgary Open
+;       Data Platform.
+;
+; CALLING SEQUENCE:
+;       aurorax_ucalgary_read(dataset, file_list)
+;
+; PARAMETERS:
+;       dataset            struct for the dataset that is being read in (retrieved from aurorax_list_dataset() function)
+;       file_list          list of files on the local computer to read in (can also be a single filename string)
+;
+; KEYWORDS:
+;       /FIRST_RECORD      only read the first record/frame/image in each file
+;       /NO_METADATA       exclude reading of metadata
+;       /QUIET             read data silently, no print messages will be shown
+;
+; OUTPUT
+;       the loaded data
+;
+; OUTPUT TYPE:
+;       a struct
+;
+; EXAMPLES:
+;       download_obj = aurorax_ucalgary_download('THEMIS_ASI_RAW','2022-01-01T06:00:00','2022-01-01T06:59:59',site_uid='gill')
+;       data = aurorax_ucalgary_read(d.dataset,f)
+;       help,data
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/index.md b/docs/code/idlaurorax_api_reference/index.md
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+---
+hide:
+  - toc
+---
+
+# IDL-AuroraX API Reference
+
+IDL-AuroraX is an IDL library for interacting with the AuroraX platform. It can be used to retrieve data such as ephemeris and data product records, and perform conjunction searches.
+
+The below pages provide the documentation for each function. Examples can be found in the over-arching "Basic Usage" and "Advanced Usage" sections.
+
+## Data Download and Reading
+
+- [`aurorax_list_datasets`](/code/idlaurorax_api_reference/data/aurorax_list_datasets/)
+- [`aurorax_list_observatories`](/code/idlaurorax_api_reference/data/aurorax_list_observatories/)
+- [`aurorax_ucalgary_get_urls`](/code/idlaurorax_api_reference/data/aurorax_ucalgary_get_urls/)
+- [`aurorax_ucalgary_download`](/code/idlaurorax_api_reference/data/aurorax_ucalgary_download/)
+- [`aurorax_ucalgary_download_best_skymap`](/code/idlaurorax_api_reference/data/aurorax_ucalgary_download_best_skymap/)
+- [`aurorax_ucalgary_read`](/code/idlaurorax_api_reference/data/aurorax_ucalgary_read/)
+- [`aurorax_ucalgary_is_read_supported`](/code/idlaurorax_api_reference/data/aurorax_ucalgary_is_read_supported/)
+
+## Analysis Support Software
+
+- [`aurorax_bounding_box_extract_metric`](/code/idlaurorax_api_reference/tools/aurorax_bounding_box_extract_metric/)
+- [`aurorax_calibrate_rego`](/code/idlaurorax_api_reference/tools/aurorax_calibrate_rego/)
+- [`aurorax_calibrate_trex_nir`](/code/idlaurorax_api_reference/tools/aurorax_calibrate_trex_nir/)
+- [`aurorax_keogram_add_axis`](/code/idlaurorax_api_reference/tools/aurorax_keogram_add_axis/)
+- [`aurorax_keogram_create_custom`](/code/idlaurorax_api_reference/tools/aurorax_keogram_create_custom/)
+- [`aurorax_keogram_create`](/code/idlaurorax_api_reference/tools/aurorax_keogram_create/)
+- [`aurorax_keogram_plot`](/code/idlaurorax_api_reference/tools/aurorax_keogram_plot/)
+- [`aurorax_mosaic_plot`](/code/idlaurorax_api_reference/tools/aurorax_mosaic_plot/)
+- [`aurorax_mosaic_oplot`](/code/idlaurorax_api_reference/tools/aurorax_mosaic_oplot/)
+- [`aurorax_mosaic_prep_images`](/code/idlaurorax_api_reference/tools/aurorax_mosaic_prep_images/)
+- [`aurorax_mosaic_prep_skymap`](/code/idlaurorax_api_reference/tools/aurorax_mosaic_prep_skymap/)
+- [`aurorax_get_decomposed_color`](/code/idlaurorax_api_reference/tools/aurorax_get_decomposed_color/)
+- [`aurorax_movie`](/code/idlaurorax_api_reference/tools/aurorax_movie/)
+
+## TREx Auroral Transport Model (ATM)
+
+- Coming soon!
+
+## AuroraX Search Engine
+- [`aurorax_conjunction_search`](/code/idlaurorax_api_reference/search/conjunctions/search/)
+- [`aurorax_open_conjunctions_in_aurorax`](/code/idlaurorax_api_reference/search/conjunctions/open_in_aurorax/)
+- [`aurorax_open_conjunctions_in_swarmaurora`](/code/idlaurorax_api_reference/search/conjunctions/open_in_swarmaurora/)
+- [`aurorax_save_swarmaurora_custom_import_file`](/code/idlaurorax_api_reference/search/conjunctions/save_swarmaurora_import_file/)
+- [`aurorax_create_advanced_distances_hash`](/code/idlaurorax_api_reference/search/conjunctions/create_advanced_distances/)
+- [`aurorax_create_criteria_block`](/code/idlaurorax_api_reference/search/conjunctions/create_criteria_block/)
+- [`aurorax_create_metadata_filter`](/code/idlaurorax_api_reference/search/metadata_filters/create_metadata_filter/)
+- [`aurorax_create_metadata_filter_expression`](/code/idlaurorax_api_reference/search/metadata_filters/create_expression/)
+- [`aurorax_data_products_availability`](/code/idlaurorax_api_reference/search/availability/data_products/)
+- [`aurorax_data_product_search`](/code/idlaurorax_api_reference/search/data_products/search/)
+- [`aurorax_ephemeris_availability`](/code/idlaurorax_api_reference/search/availability/ephemeris/)
+- [`aurorax_ephemeris_search`](/code/idlaurorax_api_reference/search/ephemeris/search/)
+- [`aurorax_sources_list`](/code/idlaurorax_api_reference/search/sources/list/)
diff --git a/docs/code/idlaurorax_api_reference/overview.md b/docs/code/idlaurorax_api_reference/overview.md
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index 9b58245..0000000
--- a/docs/code/idlaurorax_api_reference/overview.md
+++ /dev/null
@@ -1,24 +0,0 @@
----
-hide:
-  - toc
----
-
-# IDL-AuroraX API Reference
-
-IDL-AuroraX is an IDL library for interacting with the AuroraX platform. It can be used to retrieve data such as ephemeris and data product records, and perform conjunction searches.
-
-The below pages provide the documentation for each function. Examples can be found in the over-arching "Basic Usage" and "Advanced Usage" sections.
-
-- [`aurorax_conjunction_search`](/code/idlaurorax_api_reference/conjunctions/search/)
-- [`aurorax_open_conjunctions_in_aurorax`](/code/idlaurorax_api_reference/conjunctions/open_in_aurorax/)
-- [`aurorax_open_conjunctions_in_swarmaurora`](/code/idlaurorax_api_reference/conjunctions/open_in_swarmaurora/)
-- [`aurorax_save_swarmaurora_custom_import_file`](/code/idlaurorax_api_reference/conjunctions/save_swarmaurora_import_file/)
-- [`aurorax_create_advanced_distances_hash`](/code/idlaurorax_api_reference/conjunctions/create_advanced_distances/)
-- [`aurorax_create_criteria_block`](/code/idlaurorax_api_reference/conjunctions/create_criteria_block/)
-- [`aurorax_create_metadata_filter`](/code/idlaurorax_api_reference/metadata_filters/create_metadata_filter/)
-- [`aurorax_create_metadata_filter_expression`](/code/idlaurorax_api_reference/metadata_filters/create_expression/)
-- [`aurorax_data_products_availability`](/code/idlaurorax_api_reference/availability/data_products/)
-- [`aurorax_data_product_search`](/code/idlaurorax_api_reference/data_products/search/)
-- [`aurorax_ephemeris_availability`](/code/idlaurorax_api_reference/availability/ephemeris/)
-- [`aurorax_ephemeris_search`](/code/idlaurorax_api_reference/ephemeris/search/)
-- [`aurorax_sources_list`](/code/idlaurorax_api_reference/sources/list/)
diff --git a/docs/code/idlaurorax_api_reference/availability/data_products.md b/docs/code/idlaurorax_api_reference/search/availability/data_products.md
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rename from docs/code/idlaurorax_api_reference/availability/data_products.md
rename to docs/code/idlaurorax_api_reference/search/availability/data_products.md
diff --git a/docs/code/idlaurorax_api_reference/availability/ephemeris.md b/docs/code/idlaurorax_api_reference/search/availability/ephemeris.md
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rename from docs/code/idlaurorax_api_reference/availability/ephemeris.md
rename to docs/code/idlaurorax_api_reference/search/availability/ephemeris.md
diff --git a/docs/code/idlaurorax_api_reference/conjunctions/create_advanced_distances.md b/docs/code/idlaurorax_api_reference/search/conjunctions/create_advanced_distances.md
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rename from docs/code/idlaurorax_api_reference/conjunctions/create_advanced_distances.md
rename to docs/code/idlaurorax_api_reference/search/conjunctions/create_advanced_distances.md
diff --git a/docs/code/idlaurorax_api_reference/conjunctions/create_criteria_block.md b/docs/code/idlaurorax_api_reference/search/conjunctions/create_criteria_block.md
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rename from docs/code/idlaurorax_api_reference/conjunctions/create_criteria_block.md
rename to docs/code/idlaurorax_api_reference/search/conjunctions/create_criteria_block.md
diff --git a/docs/code/idlaurorax_api_reference/conjunctions/open_in_aurorax.md b/docs/code/idlaurorax_api_reference/search/conjunctions/open_in_aurorax.md
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diff --git a/docs/code/idlaurorax_api_reference/conjunctions/open_in_swarmaurora.md b/docs/code/idlaurorax_api_reference/search/conjunctions/open_in_swarmaurora.md
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diff --git a/docs/code/idlaurorax_api_reference/conjunctions/save_swarmaurora_import_file.md b/docs/code/idlaurorax_api_reference/search/conjunctions/save_swarmaurora_import_file.md
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diff --git a/docs/code/idlaurorax_api_reference/conjunctions/search.md b/docs/code/idlaurorax_api_reference/search/conjunctions/search.md
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diff --git a/docs/code/idlaurorax_api_reference/data_products/search.md b/docs/code/idlaurorax_api_reference/search/data_products/search.md
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diff --git a/docs/code/idlaurorax_api_reference/ephemeris/search.md b/docs/code/idlaurorax_api_reference/search/ephemeris/search.md
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diff --git a/docs/code/idlaurorax_api_reference/metadata_filters/create_expression.md b/docs/code/idlaurorax_api_reference/search/metadata_filters/create_expression.md
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rename from docs/code/idlaurorax_api_reference/metadata_filters/create_expression.md
rename to docs/code/idlaurorax_api_reference/search/metadata_filters/create_expression.md
diff --git a/docs/code/idlaurorax_api_reference/metadata_filters/create_metadata_filter.md b/docs/code/idlaurorax_api_reference/search/metadata_filters/create_metadata_filter.md
similarity index 100%
rename from docs/code/idlaurorax_api_reference/metadata_filters/create_metadata_filter.md
rename to docs/code/idlaurorax_api_reference/search/metadata_filters/create_metadata_filter.md
diff --git a/docs/code/idlaurorax_api_reference/sources/list.md b/docs/code/idlaurorax_api_reference/search/sources/list.md
similarity index 100%
rename from docs/code/idlaurorax_api_reference/sources/list.md
rename to docs/code/idlaurorax_api_reference/search/sources/list.md
diff --git a/docs/code/idlaurorax_api_reference/sources/stats.md b/docs/code/idlaurorax_api_reference/search/sources/stats.md
similarity index 100%
rename from docs/code/idlaurorax_api_reference/sources/stats.md
rename to docs/code/idlaurorax_api_reference/search/sources/stats.md
diff --git a/docs/code/idlaurorax_api_reference/tools/aurorax_bounding_box_extract_metric.md b/docs/code/idlaurorax_api_reference/tools/aurorax_bounding_box_extract_metric.md
new file mode 100644
index 0000000..7e71c59
--- /dev/null
+++ b/docs/code/idlaurorax_api_reference/tools/aurorax_bounding_box_extract_metric.md
@@ -0,0 +1,49 @@
+---
+hide:
+  - toc
+---
+
+# aurorax_bounding_box_extract_metric
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_BOUNDING_BOX_EXTRACT_METRIC
+;
+; PURPOSE:
+;       Extract a luminosity related metric from a portion of an image.
+;
+; EXPLANATION:
+;       Extract a metric, related to luminosity, from pixel data within
+;       some bounded region within a single or set of ASI CCD images,
+;       defined by CCD, lat/lon, elevation, or azimuth boundaries.
+;
+; CALLING SEQUENCE:
+;       aurorax_bounding_box_extract_metric(images, mode, xy_bounds)
+;
+; PARAMETERS:
+;       images          array of images to extract metric from
+;       mode            string giving the input coordinate type ("geo", "mag", "ccd", "azim", "elev")
+;       xy_bounds       a two or four element array giving the bounds of the region of interest,
+;                       for the desired mode ([lon0,lon1,lat0,lat1], [min_elev,max_elev], ... etc.)
+;       metric          the metric to compute, accepted is "median" (default), "mean", or "sum"
+;       time_stamp      the timestamp to use for magnetic coordinate conversions, optional
+;       skymap          the skymap to use for georeferencing, optional
+;       altitude_km     the altitude of the image data for georeferencing, optional
+;       n_channels      manually specify the image data channels, otherwise its estimated based on shape, optional
+;
+; KEYWORDS:
+;       /SHOW_PREVIEW   plot a preview of the bounded area on top of the first image frame
+;
+; OUTPUT
+;       extracted metric for all frames provided
+;
+; OUTPUT TYPE:
+;       array
+;
+; EXAMPLES:
+;       luminosity = aurorax_bounding_box_extract_metric(images, "geo", [-94, -95, 55, 55.5], skymap=skymap, altitude_km=110)
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/tools/aurorax_calibrate_rego.md b/docs/code/idlaurorax_api_reference/tools/aurorax_calibrate_rego.md
new file mode 100644
index 0000000..32bf574
--- /dev/null
+++ b/docs/code/idlaurorax_api_reference/tools/aurorax_calibrate_rego.md
@@ -0,0 +1,45 @@
+---
+hide:
+  - toc
+---
+
+# aurorax_calibrate_rego
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_CALIBRATE_REGO
+;
+; PURPOSE:
+;       Calibrate one or more REGO images.
+;
+; EXPLANATION:
+;       Apply a number of calibrations, such as dark frame subtraction,
+;       flatfield calibration, and calibration to Rayleighs, one can
+;       apply only certain calibration steps if desired.
+;
+; CALLING SEQUENCE:
+;       aurorax_calibrate_rego(images, cal_flatfield, cal_rayleighs)
+;
+; PARAMETERS:
+;       images                  array of images to calibrate
+;       cal_flatfield           the flatfield calibration to use (if desired), usually a result of reading a calibration file, optional
+;       cal_rayleighs           the rayleighs calibration to use (if desired), usually a result of reading a calibration file, optional
+;       exposure_length_sec     the exposure length for the image data being calibrated, optional (defaults to 3.0)
+;
+; KEYWORDS:
+;       /NO_DARK_SUBTRACT       omits the dark subtraction step of the calibration process
+;
+; OUTPUT
+;       calibrated image data
+;
+; OUTPUT TYPE:
+;       array
+;
+; EXAMPLES:
+;       rayleighs_images = aurorax_calibrate_rego(images, cal_flatfield=flatfield_cal, cal_rayleighs=rayleighs_cal)
+;       bg_subtracted_images = aurorax_calibrate_rego(images)
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/tools/aurorax_calibrate_trex_nir.md b/docs/code/idlaurorax_api_reference/tools/aurorax_calibrate_trex_nir.md
new file mode 100644
index 0000000..3e26277
--- /dev/null
+++ b/docs/code/idlaurorax_api_reference/tools/aurorax_calibrate_trex_nir.md
@@ -0,0 +1,45 @@
+---
+hide:
+  - toc
+---
+
+# aurorax_calibrate_trex_nir
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_CALIBRATE_TREX_NIR
+;
+; PURPOSE:
+;       Calibrate one or more TREx NIR images.
+;
+; EXPLANATION:
+;       Apply a number of calibrations, such as dark frame subtraction,
+;       flatfield calibration, and calibration to Rayleighs, one can
+;       apply only certain calibration steps if desired.
+;
+; CALLING SEQUENCE:
+;       aurorax_calibrate_trex_nir(images, cal_flatfield, cal_rayleighs)
+;
+; PARAMETERS:
+;       images                  array of images to calibrate
+;       cal_flatfield           the flatfield calibration to use (if desired), usually a result of reading a calibration file, optional
+;       cal_rayleighs           the rayleighs calibration to use (if desired), usually a result of reading a calibration file, optional
+;       exposure_length_sec     the exposure length for the image data being calibrated, optional (defaults to 5.0)
+;
+; KEYWORDS:
+;       /NO_DARK_SUBTRACT       omits the dark subtraction step of the calibration process
+;
+; OUTPUT
+;       calibrated image data
+;
+; OUTPUT TYPE:
+;       array
+;
+; EXAMPLES:
+;       rayleighs_images = aurorax_calibrate_trex_nir(images, cal_flatfield=flatfield_cal, cal_rayleighs=rayleighs_cal)
+;       bg_subtracted_images = aurorax_calibrate_trex_nir(images)
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/tools/aurorax_get_decomposed_color.md b/docs/code/idlaurorax_api_reference/tools/aurorax_get_decomposed_color.md
new file mode 100644
index 0000000..5134332
--- /dev/null
+++ b/docs/code/idlaurorax_api_reference/tools/aurorax_get_decomposed_color.md
@@ -0,0 +1,40 @@
+---
+hide:
+  - toc
+---
+
+# aurorax_get_decomposed_color
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_GET_DECOMPOSED_COLOR
+;
+; PURPOSE:
+;       Convert RGB triple to decomposed long integer format.
+;
+; EXPLANATION:
+;       This function is useful for plotting in decomposed color mode.
+;       It converts an RGB triple to a long integer that can be used
+;       to plot the corresponding color in decomposed color mode.
+;
+; CALLING SEQUENCE:
+;       aurorax_get_decomposed_color([r,g,b])
+;
+; PARAMETERS:
+;       rgb_triple        a three element array specifying the RGB color to convert
+;
+; KEYWORDS:
+;
+; OUTPUT
+;       the decomposed long integer representation of the color
+;
+; OUTPUT TYPE:
+;       long
+;
+; EXAMPLES:
+;       long_cyan = aurorax_get_decomposed_color([0,255,255])
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/tools/aurorax_keogram_add_axis.md b/docs/code/idlaurorax_api_reference/tools/aurorax_keogram_add_axis.md
new file mode 100644
index 0000000..f7b9279
--- /dev/null
+++ b/docs/code/idlaurorax_api_reference/tools/aurorax_keogram_add_axis.md
@@ -0,0 +1,45 @@
+---
+hide:
+  - toc
+---
+
+# aurorax_keogram_add_axis
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_KEOGRAM_ADD_AXIS
+;
+; PURPOSE:
+;       Add a georeferenced axis to a keogram structure.
+;
+; EXPLANATION:
+;       Add one or more desired physical axes to a keogram structure, which is
+;       usually obtained via aurorax_keogram_create. Options are elevation, and
+;       geographic/magnetic lats (lons for ewograms).
+;
+; CALLING SEQUENCE:
+;       aurorax_keogram_add_axis(keogram_struct, skymap, /axis_type)
+;
+; PARAMETERS:
+;       keogram_struct      keogram structure - usually the return value of aurorax_keogram_create()
+;       skymap              the skymap to use for georeferencing
+;       altitude_km         altitude, in kilometers, of the keogram data, optional
+;
+; KEYWORDS:
+;       /GEO        adds an axis of geographic coordinates
+;       /GEO        adds an axis of geomagnetic coordinates
+;       /GEO        adds an axis of elevation angles
+;
+; OUTPUT
+;       keogram structure containing new axes
+;
+; OUTPUT TYPE:
+;       struct
+;
+; EXAMPLES:
+;       keo = aurorax_keogram_add_axis(keo, skymap, /geo, /elev, altitude_km=110)
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/tools/aurorax_keogram_create.md b/docs/code/idlaurorax_api_reference/tools/aurorax_keogram_create.md
new file mode 100644
index 0000000..102c5fa
--- /dev/null
+++ b/docs/code/idlaurorax_api_reference/tools/aurorax_keogram_create.md
@@ -0,0 +1,41 @@
+---
+hide:
+  - toc
+---
+
+# aurorax_keogram_create
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_KEOGRAM_CREATE
+;
+; PURPOSE:
+;       Create a keogram object.
+;
+; EXPLANATION:
+;       Create a keogram structure from an array of image data.
+;
+; CALLING SEQUENCE:
+;       aurorax_keogram_create(img, time_stamp)
+;
+; PARAMETERS:
+;       images          array of images to extract metric from
+;       time_stamp      array of timestamps corresponding to each frame in images
+;       axis            the axis index (1 or 0) to slice the keogram from - defualt is 1 (N-S slice)
+;
+; KEYWORDS:
+;
+; OUTPUT
+;       keogram object structure containing data and axes
+;
+; OUTPUT TYPE:
+;       struct
+;
+; EXAMPLES:
+;       keogram = aurorax_keogram_create(img, time_stamp)
+;       ewogram = aurorax_keogram_create(img, time_stamp, axis=1)
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/tools/aurorax_keogram_create_custom.md b/docs/code/idlaurorax_api_reference/tools/aurorax_keogram_create_custom.md
new file mode 100644
index 0000000..bf4fd4f
--- /dev/null
+++ b/docs/code/idlaurorax_api_reference/tools/aurorax_keogram_create_custom.md
@@ -0,0 +1,49 @@
+---
+hide:
+  - toc
+---
+
+# aurorax_keogram_create_custom
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_KEOGRAM_CREATE_CUSTOM
+;
+; PURPOSE:
+;       Create a keogram from a custom slice of image data.
+;
+; EXPLANATION:
+;       Create a keogram by slicing image data along a custom contour
+;       defined by lats/lons or CCD coordintes.
+;
+; CALLING SEQUENCE:
+;       aurorax_keogram_create_custom(images, time_stamp, "ccd", x_locs, y_locs)
+;
+; PARAMETERS:
+;       images                array of images to extract metric from
+;       time_stamp            array of timestamps corresponding to each image frame
+;       coordinate_system     a string giving the coordinate system ("ccd", "geo", "mag")
+;       x_locs                the x locations, in desired coordinate system, to slice keogram along
+;       y_locs                the y locations, in desired coordinate system, to slice keogram along
+;       width                 the width of the keogram slice, in pixel units, optional (defaults to 2)
+;       skymap                the skymap to use for georeferencing, optional
+;       altitude_km           the altitude of the image data for georeferencing, optional
+;       metric                the metric to use to compute each keogram pixel "median" (default), "mean", or "sum", optional
+;
+; KEYWORDS:
+;       /SHOW_PREVIEW         plot a preview of the keogram slice on top of the first image frame
+;
+; OUTPUT
+;       custom keogram structure containing keogram data and temporal axis
+;
+; OUTPUT TYPE:
+;       struct
+;
+; EXAMPLES:
+;       ccd_keo = aurorax_keogram_create_custom(img, time_stamp, "ccd", x_arr, y_arr, width=5, metric="sum", /show_preview)
+;       geo_keo = aurorax_keogram_create_custom(img, time_stamp, "geo", longitudes, latitudes, skymap=skymap, altitude_km=113)
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/tools/aurorax_keogram_plot.md b/docs/code/idlaurorax_api_reference/tools/aurorax_keogram_plot.md
new file mode 100644
index 0000000..8dec81f
--- /dev/null
+++ b/docs/code/idlaurorax_api_reference/tools/aurorax_keogram_plot.md
@@ -0,0 +1,46 @@
+---
+hide:
+  - toc
+---
+
+# aurorax_keogram_plot
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_KEOGRAM_PLOT
+;
+; PURPOSE:
+;       Plot a keogram object.
+;
+; EXPLANATION:
+;       Plot keogram data, adding axes stored in the keogram
+;       structure as desired, defaults to CCD axis.
+;
+; CALLING SEQUENCE:
+;       aurorax_keogram_plot, keogram_struct, /keyword_args
+;
+; PARAMETERS:
+;       keogram_struct      keogram object to plot, usually the return value of aurorax_keogram_create()
+;       title               string giving the plot title, optional
+;       dimensions          two-element array giving dimensions of the plotting window in device coordinates, optional
+;       location            two-element array giving location of the plotting window in device coordinates, optional
+;       x_tick_interval     interval between ticks on the x-axis, optional (default is 200)
+;       y_tick_interval     interval between ticks on the y-axis, optional (default is 50)
+;       aspect_ratio        float giving the aspect ratio to display keogram data
+;
+; KEYWORDS:
+;       /GEO                labels geographic coordinates on the y-axis (axis must exist in keogram structure)
+;       /MAG                labels geomagnetic coordinates on the y-axis (axis must exist in keogram structure)
+;       /ELEV               labels elevation angles on the y-axis (axis must exist in keogram structure)
+;
+; OUTPUT
+;
+; OUTPUT TYPE:
+;
+; EXAMPLES:
+;       aurorax_keogram_plot, keo, title="Geographic", /geo, location=[0,0], dimensions=[1000,400]
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/tools/aurorax_mosaic_oplot.md b/docs/code/idlaurorax_api_reference/tools/aurorax_mosaic_oplot.md
new file mode 100644
index 0000000..0aa8011
--- /dev/null
+++ b/docs/code/idlaurorax_api_reference/tools/aurorax_mosaic_oplot.md
@@ -0,0 +1,47 @@
+---
+hide:
+  - toc
+---
+
+# aurorax_mosaic_oplot
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_MOSAIC_OPLOT
+;
+; PURPOSE:
+;       Plot lines of constant lat/lon, and custom points on a mosaic.
+;
+; EXPLANATION:
+;       Plot either, or a combination of, lines of constant geographic or
+;       geomagnetic latitude and/or longitude. Can also be used to plot
+;       a single point in geographic or geomagnetic coordinates.
+;
+; CALLING SEQUENCE:
+;       aurorax_mosaic_oplot, constant_lats=lats, constant_lons=lons, point=[lon,lat]
+;
+; PARAMETERS:
+;       constant_lats     a scalar or array giving latitude(s) to add constant lines, optional
+;       constant_lots     a scalar or array giving longitude(s) to add constant lines, optional
+;       point             a two element array specifying the lon, lat to plot, optional
+;       color             long integer giving the color to plot in, optional (default is 0 i.e. black)
+;       thick             integer giving line thickness for any lines plotted, optional (default is 1)
+;       linestyle         integer giving IDL linestyle, optional (default is 0, i.e. solid)
+;       symbol            integer giving IDL symbol, optional (default is 0, i.e. none for lines and circle for point)
+;       symsize           integer giving IDL symbol size, optional (default is 1)
+;
+; KEYWORDS:
+;       /MAG              specify that coordinates are given in geomagnetic coordinates (default is geographic)
+;
+; OUTPUT
+;
+; OUTPUT TYPE:
+;
+; EXAMPLES:
+;       aurorax_mosaic_oplot, point=[245,61.2], color=aurorax_get_decomposed_color([0,0,255])
+;       aurorax_mosaic_oplot, constant_lats=[40,50,60], constant_lons=[220,240,260], linestyle=2, thick=3
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/tools/aurorax_mosaic_plot.md b/docs/code/idlaurorax_api_reference/tools/aurorax_mosaic_plot.md
new file mode 100644
index 0000000..e544f2a
--- /dev/null
+++ b/docs/code/idlaurorax_api_reference/tools/aurorax_mosaic_plot.md
@@ -0,0 +1,50 @@
+---
+hide:
+  - toc
+---
+
+# aurorax_mosaic_plot
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_MOSAIC_PLOT
+;
+; PURPOSE:
+;       Create a mosaic
+;
+; EXPLANATION:
+;       Plot a mosaic onto a pre-defined map window, using *prepared*
+;       image data and skymaps.
+;
+; CALLING SEQUENCE:
+;       aurorax_mosaic_plot, prepped_data, prepped_skymap, image_idx, min_elevation=5
+
+;
+; PARAMETERS:
+;       prepped_data          single, or array of 'prepped_data' structures (the return of aurorax_mosaic_prep_data())
+;       prepped_skymaps       single, or array of 'prepped_data' structures (the return of aurorax_mosaic_prep_data())
+;       frame_idx             integer specifying the frame idx of image data that is to be plotted
+;       min_elevation         int/float, or array (same length as prepped_data) of ints/floats specifying the minimum
+;                             elevation in degrees to begin plotting data, optional (default is 5 deg)
+;       intensity_scales      a two element array, or hash of two element arrays (for scaling on a per-site basis),
+;                             giving the min/max scale bounds for data (default is [0,20000])
+;       colortable            an integer, or array of integers with the same length as prepped_data, specifying the
+;                             IDL colortable to plot data with, optional (default is 0, i.e. gray)
+;       elevation_increment   a parameter that affects the plotting algorithm - the default is 0.25 - increasing this
+;                             parameter can speed up plotting, and decreasing it can help make boundaries between sites
+;                             more distinct (if they appear to be getting blended)
+;
+; KEYWORDS:
+;
+; OUTPUT
+;
+; OUTPUT TYPE:
+;
+; EXAMPLES:
+;       aurorax_mosaic_plot, prepped_data, prepped_skymap, image_idx, min_elevation=7, intensity_scales=[500,10000], colortable=3
+;
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/tools/aurorax_mosaic_prep_images.md b/docs/code/idlaurorax_api_reference/tools/aurorax_mosaic_prep_images.md
new file mode 100644
index 0000000..a0f21c1
--- /dev/null
+++ b/docs/code/idlaurorax_api_reference/tools/aurorax_mosaic_prep_images.md
@@ -0,0 +1,41 @@
+---
+hide:
+  - toc
+---
+
+# aurorax_mosaic_prep_images
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_MOSAIC_PREP_IMAGES
+;
+; PURPOSE:
+;       Prepare image data to create a mosaic
+;
+; EXPLANATION:
+;       Takes image data and formats it in a way such that it
+;       can be fed into the aurorax_mosaic_plot routine
+;
+; CALLING SEQUENCE:
+;       aurorax_mosaic_prep_images(list(img_data1, image_data2))
+;
+; PARAMETERS:
+;       image_data        a list of image data objects, where each object is usually the return
+;                         value of aurorax_ucalgary_read(). Note that even if preparing a single
+;                         image data object, it must be enclosed in a list.
+;
+; KEYWORDS:
+;
+; OUTPUT
+;       a prepped_data structure
+;
+; OUTPUT TYPE:
+;       struct
+;
+; EXAMPLES:
+;       prepped_data = aurorax_prep_images(list(aurorax_ucalgary_read(d.dataset, d.filenames)))
+;+
+;-------------------------------------------------------------
+```
\ No newline at end of file
diff --git a/docs/code/idlaurorax_api_reference/tools/aurorax_mosaic_prep_skymap.md b/docs/code/idlaurorax_api_reference/tools/aurorax_mosaic_prep_skymap.md
new file mode 100644
index 0000000..6da36c3
--- /dev/null
+++ b/docs/code/idlaurorax_api_reference/tools/aurorax_mosaic_prep_skymap.md
@@ -0,0 +1,43 @@
+---
+hide:
+  - toc
+---
+
+# aurorax_mosaic_prep_skymap
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_MOSAIC_PREP_SKYMAPS
+;
+; PURPOSE:
+;       Prepare skymaps to create a mosaic
+;
+; EXPLANATION:
+;       Takes skymap(s) and formats them in a way such that they
+;       can be fed into the aurorax_mosaic_plot routine
+;
+; CALLING SEQUENCE:
+;       aurorax_mosaic_prep_skymap(list(skymap1, skymap2))
+;
+; PARAMETERS:
+;       image_data        a list of skymap data objects, where each object is usually the return
+;                         value of aurorax_ucalgary_read(). Note that even if preparing a single
+;                         skymap object, it must be enclosed in a list.
+;       altitude_km       the altitude (in kilometers) at which the image data should be
+;                         prepared for mosaicking
+;
+; KEYWORDS:
+;
+; OUTPUT
+;       a prepped_skymap structure
+;
+; OUTPUT TYPE:
+;       struct
+;
+; EXAMPLES:
+;       prepped_skymap = aurorax_prep_skymaps(list(aurorax_ucalgary_read(d.dataset, d.filenames)))
+;+
+;-------------------------------------------------------------
+```
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diff --git a/docs/code/idlaurorax_api_reference/tools/aurorax_movie.md b/docs/code/idlaurorax_api_reference/tools/aurorax_movie.md
new file mode 100644
index 0000000..b1baeb2
--- /dev/null
+++ b/docs/code/idlaurorax_api_reference/tools/aurorax_movie.md
@@ -0,0 +1,39 @@
+---
+hide:
+  - toc
+---
+
+# aurorax_movie
+
+```
+;-------------------------------------------------------------
+;+
+; NAME:
+;       AURORAX_MOVIE
+;
+; PURPOSE:
+;       Create a movie.
+;
+; EXPLANATION:
+;       Given a list of filenames referencing images, create and
+;       save a movie.
+;
+; CALLING SEQUENCE:
+;       aurorax_movie, input_filenames, output_filename, fps
+;
+; PARAMETERS:
+;       input_filenames     an array of strings giving filenames of all images
+;       output_filenames    the filename location at which to save the image
+;       fps                 integer giving the frames per second to create movie at
+;
+; KEYWORDS:
+;
+; OUTPUT
+;
+; OUTPUT TYPE:
+;
+; EXAMPLES:
+;       aurorax_create_movive, file_search("path\to\images\*.png"), "movie.mp4", 30
+;+
+;-------------------------------------------------------------
+```
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